Hi Shawn,
Thanks for this post with additional information. As this is a single controller implementation, the first thing to consider is aggregate configuration.
The 2 x DS4246 contains 48 drives. Allowing two drives spare, I would create an aggregate of 2 x 22 disk RAID-DP RAID groups. I would call it aggr1sas600ext
If the FAS2650 chassis contains additional disks, they should be in their own aggregate - maybe aggr1sas600int
Once underlaying RAID and aggregates are setup, then you setup port channels, IPs and VLANs.
I would create at least three SVMs - one for log data (svmLOG), one for iSCSI (svmBlock) and one for VMs.
On each VM, you setup storage protocols - NFS and iSCSI based on your description. Then define which hosts can access each protocol.
All of this can be done via the built in web-based GUI - OnCommand System Manager.
Other things to look at are snapshot schedules, and our training courses at http://learningcenter.netapp.com
Hope this helps!